Electrospray ionization mass spectrometry (ESI-MS) has become an important technique for the analysis of biopolymers. The multiple charging phenomenon allows fast, accurate and precise molecular mass measurement, identification of modifications and more detailed structural studies for very high-mass biopolymers.
Amplification of specific DNA sequences utilizing the polymerase chain reaction has widespread applications in many scientific disciplines, including microbiology, medical research, forensic analysis, and clinical diagnostics. Most often, PCR products are “sized” using traditional biochemical techniques such as standard gel electrophoresis using either intercalating dyes or fluorescently labeled primers. The Taqman™ assay, which is widely used in a number of PCR-based diagnostic kits, confirms the presence (or absence) of a specific PCR product but provides no direct readout on the size of the amplicon. So-called “real-time” PCR devices, which measure the laser-induced fluorescence of the PCR product during the amplification cycles, are used to quantify the amplification of DNA from a given DNA template and primer set. These methods have limited utility for relatively small amplicons (less than 150 base pairs), owing to the proportionately high fluorescence background, and do not provide any information with respect to amplicon heterogeneity or exact length.
Compared to these more traditional methods, mass spectrometry has several potential advantages as a platform on which to characterize PCR products, including speed, sensitivity, and mass accuracy. Because the exact mass of each of the bases which comprise DNA is known with great accuracy, a high-precision mass measurement obtained via mass spectrometry can be used to derive a base composition within the experimentally obtained mass measurement uncertainty (J. Aaserud, Z. Guan, D. P. Little and F. W. McLafferty, Int. J. Mass Spectrom. Ion Processes, 1997, 167/168, 705-712. and D. C. Muddiman, G. A. Anderson, S. A. Hofstadler and R. D. Smith, Anal. Chem. 1997, 69, 1543-1549). Methods for rapid identification of unknown bioagents using a combination of nucleic acid amplification and determination of base composition of informative amplicons by molecular mass analysis are disclosed and claimed in published U.S. Patent applications 20030027135, 20030082539, 20030124556, 20030175696, 20030175695, 20030175697, and 20030190605 and U.S. patent application Ser. Nos. 10/326,047, 10/660,997, 10/660,122 and 10/660,996, all of which are commonly owned and incorporated herein by reference in entirety.
Both MALDI (matrix assisted, laser desorption ionization) and electrospray (ESI) mass spectrometry have been employed to ionize PCR products for subsequent mass spectrometric detection. While MALDI is widely used to analyze short (20-mer or smaller) oligonucleotides, applications to amplicons in excess of 100 bp are less common. ESI is one of the most widely used ionization techniques for large biological molecules owing to the inherent “softness” of the ionization process, which allows DNA in excess of 500 bp to be ionized without dissociation.
In ESI, large charged droplets are produced in the process of “pneumatic nebulization” where the analyte solution is forced through a needle at the end of which is applied a potential sufficient to disperse the emerging solution into a very fine spray of charged droplets all of which have the same polarity. The solvent evaporates, shrinking the droplet size and increasing the charge concentration at the droplet's surface. Eventually, at the Rayleigh limit, Coulombic repulsion overcomes the droplet's surface tension and the droplet explodes. This “Coulombic explosion” forms a series of smaller, lower charged droplets. The process of shrinking followed by explosion is repeated until individually charged analyte ions are formed. The charges are statistically distributed amongst the analyte's available charge sites, leading to the possible formation of multiply charged ions conditions. Increasing the rate of solvent evaporation, by introducing a drying gas flow counter current to the sprayed ions, increases the extent of multiple-charging. Decreasing the capillary diameter and lowering the analyte solution flow rate i.e. in nanospray ionization, will create ions with higher m/z ratios (i.e. it is a softer ionization technique) than those produced by “conventional” ESI and are of much more use in the field of bioanalysis.
Unfortunately, ESI requires relatively clean samples and is notoriously intolerable of cationic salts, detergents, and many buffering agents commonly used in biochemical laboratories.
The buffer system commonly employed in the polymerase chain reaction includes electrospray incompatible reagents such as 50 mM KCl, 2 mM MgCl2, 10 mM Tris-HCl, and each of the four deoxynucleotide triphosphates (dNTPs) at 200:M. Even the presence of relatively low concentrations of metal cations (less than 100:M) can significantly reduce MS sensitivity for oligonucleotides as the signal for each molecular ion is spread out over multiple salt adducts. Thus, in addition to removing detergents and dNTPs, effective ESI-MS of PCR products requires that the salt concentration be reduced by more than a factor of 1000 prior to analysis.
Ethanol precipitation has been used to desalt PCR products for subsequent MS analysis as short oligonucleotides and salts are removed while the sample is concentrated (M. T. Krahmer, Y. A. Johnson, J. J. Walters, K. F. Fox, A. Fox and M. Nagpal, Electrospray Anal. Chem. 1999, 71, 2893-2900; T. Tsuneyoshi, K. Ishikawa, Y. Koga, Y. Naito, S. Baba, H. Terunuma, R. Arakawa and D. J. Prockop Rapid Commun. Mass Spectrom. 1997, 11, 719-722; and D. C. Muddiman, D. S. Wunschel, C. L. Liu, L. Pasatolic, K. F. Fox, A. Fox, G. A. Anderson and R. D. Smith Anal. Chem. 1996, 68, 3705-3712). In this method, the PCR product can be precipitated from concentrated ammonium acetate solutions, either overnight at 5° C. or over the course of 10-15 min with cold (−20° C.) ethanol. Unfortunately, a precipitation step alone is generally insufficient to obtain PCR products which are adequately desalted to obtain high-quality ESI spectra; consequently, precipitation is generally followed by a dialysis step to further desalt the sample (D. C. Muddiman, D. S. Wunschel, C. L. Liu, L. Pasatolic, K. F. Fox, A. Fox, G. A. Anderson and R. D. Smith Anal. Chem. 1996, 68, 3705-3712). While several researchers have successfully employed these methods to characterize a number of PCR products, the route to applying these methods in a robust and fully automated high-throughput manner is not obvious.
Commercial DNA purification kits may also be used in conjunction with traditional desalting techniques such as microdialysis (S. Hahner, A. Schneider, A. Ingendoh and J. Mosner Nucleic Acids Res. 2000, 28, e82/i-e82/viii; and A. P. Null, L. T. George and D. C. Muddiman J. Am. Soc. Mass Spectrom. 2002, 13, 338-344). Other purification techniques, such as gel electrophoresis followed by high-performance liquid chromatography or drop dialysis, or cation exchange using membranes or resins have also been used to obtain high-purity, desalted DNA for MS detection (L. M. Benson, S.-S. Juliane, P. D. Rodringues, T. Andy, L. J. Maher III and S. Naylor, In: The 47th ASMS Conference on Mass Spectrometry and Allied Topics, Dallas, Tex. (1999); C. G. Huber and M. R. Buchmeiser Anal. Chem. 1998, 70, 5288-5295; H. Oberacher, W. Parson, R. Muehlmann and C. G. Huber Anal. Chem. 2001, 73, 5109-5115; and C. J. Sciacchitano J. Liq. Chromatogr. Relat. Technol. 1996, 19, 2165-2178). Unfortunately, as with the techniques described above, the path toward a rapid and fully automated high-throughput implementation is not obvious.
Jiang and Hofstadler have developed and reported a single protocol for the purification and desalting of PCR products which employs commercially available pipette tips packed with anion exchange resin (Y. Jiang and S. A. Hofstadler Anal. Biochem. 2003, 316, 50-57). This protocol yields an ESI-MS-compatible sample and requires only 10:1 of crude PCR product. However, the method is cost-prohibitive when applied to high volume and high throughput processes such as the methods cited above for identification of unknown bioagents. Retail costs of using the commercially-obtained ZipTip™ AX (Millipore Corp. Bedford, Mass.) are estimated at $1.77 per plate well.
There remains a need for a method of purification of nucleic acids for mass spectrometry which is rapid, efficient and non-cost prohibitive. The present invention satisfies this need.
Solution capture of nucleic acids such as those obtained from amplification reactions has enabled a rapid, cost-effective method of extracting and purifying these analytes for subsequent analysis by mass spectrometry. Since the nucleic acids and the anion exchange media are in solution, efficient capture of the nucleic acids is accomplished by vortexing, or other mixing methods. This has eliminated the need to pack the media in a column format which would require multiple passes of the nucleic acid solution over it to achieve high levels of recovery of nucleic acids. While longer columns require fewer passes, significant backpressure becomes a problem. The process of packing an anion exchange resin in a column or pipette tip format increases the cost associated with the procedure accordingly. Thus the use of solution capture for purification of PCR products for analysis by mass spectrometry has substantially reduced the cost associated with sample preparation by eliminating the need to pack, equilibrate, and test a column. The retail cost of the current procedure using a pipette tip packed with anion exchange resin exemplified by ZipTip™ AX (Millipore, Bedford, Mass.) is approximately $1.77 per pipette tip (for each sample). The estimated cost of solution capture of PCR products is $0.10 per sample and takes into account the combination of anion exchange resin and filter plate. Furthermore, the time required for solution capture purification of PCR products is approximately 10 minutes per 96 well plate in contrast to the previous method which employs the ZipTip™ AX pipette tips and requires approximately 20 minutes.